When I went in 2009, I crossed in Elat and got a taxi to take me through the buffer zone as you cannot walk it (for Israels safety.) When across, the taxi driver had a friend that he called who took me to Petra. The drive was almost 2 hours long and the ride was around ~100 USD. Getting a better price on the way back was easy. Just asked people in my hotel and restaurants if they knew anybody. My friend who is Israeli had no problems with anyone when he was there either.
over 2 years ago